A parsing tool for AMP tools.
Project description
AMPcombi : Antimicorbial peptides parsing and functional classification tool
This tool parses the results of amp prediction tools into a single table and aligns the hits against a reference database of antimicrobial peptides for functional classifications.
For parsing: AMpcombi is developed to parse the output of these amp prediction tools:
Tool | Version | Link |
---|---|---|
Ampir | 1.1.0 | https://github.com/Legana/ampir |
AMPlify | 1.0.3 | https://github.com/bcgsc/AMPlify |
Macrel | 1.1.0 | https://github.com/BigDataBiology/macrel |
HMMsearch | 3.3.2 | https://github.com/EddyRivasLab/hmmer |
EnsembleAMPpred | - | https://pubmed.ncbi.nlm.nih.gov/33494403/ |
NeuBI | - | https://github.com/nafizh/NeuBI |
For classification: AMPcombi is developed to offer functional annotation of the detcted AMPs by alignemnt to AMP reference databases, for e.g.,:
Tool | Version | Link |
---|---|---|
DRAMP | 3.0 | https://github.com/CPU-DRAMP/DRAMP-3.0 |
Alignment to the reference database is done using diamond blastp v.2.0.15
======================
Installation
======================
To install AMPcombi:
Add dependencies of the tool; python > 3.0, biopython, pandas and diamond. Installation can be done using:
- pip installation
pip install AMPcombi
- git repository
git clone https://github.com/Darcy220606/AMPcombi.git
- conda
conda env create -f ampcombi/environment.yml
or
conda install AMPcombi
======================
Usage:
======================
There are two basic commands to run AMPcombi:
- Using
--amp_results
ampcombi --amp_results path/to/my/result_folder/
Here the head folder containing output files has to be given. AMPcombi finds and summarizes the output files from different tools, if the folder is structured and named as: /result_folder/toolsubdir/samplesubdir/sample.tool.filetype
.
- Note that the filetype ending might vary and can be specified with
--tooldict
, if it is different from the default.
amp_results/
├── tool_1/
| ├── sample_1/
| | └── sample_1.tool_1.tsv
| └── sample_2/
| | └── sample_2.tool_1.tsv
├── tool_2/
| ├── sample_1/
| | └── sample_1.tool_2.txt
| └── sample_2/
| | └── sample_2.tool_2.txt
├── tool_3/
├── sample_1/
| └── sample_1.tool_3.predict
└── sample_2/
└── sample_2.tool_3.predict
- Using
--path_list
and--sample_list
ampcombi --path_list [[list of paths to sample_1-outputs][list of paths to sample_2-outputs]] --sample_list [sample_1, sample_2]
Here the paths to the output-files to be summarized can be given as a list for each sample. Together with this option a list of sample-names has to be supplied.
Input options:
command | definition | default | example |
---|---|---|---|
--amp_results | path to the folder containing different tool's output files | ./test_files/ | ../amp_results |
--sample_list | list of samples' names | [] | [sample_1, sample_2] |
--path_list | list of paths to output files | [] | [[paths to sample_1 output], [paths to sample_2 outputs]] |
--outdir | name of the output directory | ./ampcombi_results/ | ./ampcombi_results/ |
--cutoff | probability cutoff to filter AMPs | 0 | 0.5 |
--faa_folder | path to the folder containing the samples` .faa files, Filenames have to contain the corresponding sample-name, i.e. sample_1.faa | ./test_faa/ | ./faa_files/ |
--tooldict | dictionary of AMP-tools and their respective output file endings | {'ampir':'ampir.tsv', 'amplify':'amplify.tsv', 'macrel':'macrel.tsv', 'hmmer_hmmsearch':'hmmsearch.txt', 'ensembleamppred':'ensembleamppred.txt'} | - |
--amp_database | path to the folder containing the reference database files: (1) a fasta file with <.fasta> file extension and (2) the corresponding table with with functional and taxonomic classifications in <.tsv> file extension | DRAMP 'general amps' database | ./amp_ref_database/ |
- Note: The fasta file corresponding to the AMP database should not contain any characters other than ['A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W',',Y']
- Note: The refernce database table should be tab delimited.
======================
Contribution:
======================
AMPcombi is a tool developed for parsing results from published AMP prediction tools. We therfore welcome fellow contributers who would like to add new AMP prediction tools results for parsing and alignment.
Adding a new tool to AMPcombi
In ampcombi/reformat_tables.py
- add a new tool function to read the output to a pandas dataframe
- add the new function to the
read_path
function
In ampcombi/main.py
- add your default
tool:tool.fileending
to the default of--tooldict
======================
Authors: @louperelo and @darcy220606
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